------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 FLAVOR=py39 UNAME_r=6.5 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/construction/biology/py-bx-python XDG_CONFIG_HOME=/construction/biology/py-bx-python XDG_CACHE_HOME=/construction/biology/py-bx-python/.cache HOME=/construction/biology/py-bx-python TMPDIR="/tmp" PATH=/construction/biology/py-bx-python/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/py-bx-python/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/py-bx-python XDG_CONFIG_HOME=/construction/biology/py-bx-python XDG_CACHE_HOME=/construction/biology/py-bx-python/.cache HOME=/construction/biology/py-bx-python TMPDIR="/tmp" PATH=/construction/biology/py-bx-python/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/py-bx-python/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/py-bx-python/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=6.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/bx-python" EXAMPLESDIR="share/examples/bx-python" DATADIR="share/bx-python" WWWDIR="www/bx-python" ETCDIR="etc/bx-python" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bx-python DOCSDIR=/usr/local/share/doc/bx-python EXAMPLESDIR=/usr/local/share/examples/bx-python WWWDIR=/usr/local/www/bx-python ETCDIR=/usr/local/etc/bx-python SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes DFLY_STING_XFAIL=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_COMPRESSION_FORMAT=.tgz DEVELOPER=1 WITH_CCACHE_BUILD=yes CCACHE_DIR=/ccache UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600503 OSVERSION=9999999 OSREL=6.5 _OSRELEASE=6.5-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=13 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/metis-5.1.0_9.pkg ===== Message from metis-5.1.0_9: -- ===> NOTICE: The metis port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing Installing /packages/All/indexinfo-0.3.1.pkg Installing /packages/All/gmp-6.2.1.pkg Installing /packages/All/mpfr-4.2.0_1,1.pkg Installing /packages/All/mpc-1.3.1_1.pkg UNFLAVORED devel/binutils -> use devel/binutils@native Installing /packages/All/liblz4-1.9.4,1.pkg Installing /packages/All/zstd-1.5.5.pkg Installing /packages/All/gettext-runtime-0.21.1.pkg Installing /packages/All/binutils-2.40_4,1.pkg Installing /packages/All/gcc12-12.2.0_6.pkg ===== Message from gcc12-12.2.0_6: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc12 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/openblas-0.3.20_1,1.pkg Installing /packages/All/suitesparse-config-7.0.1_1.pkg Installing /packages/All/suitesparse-amd-3.0.3_1.pkg Installing /packages/All/suitesparse-camd-3.0.3_1.pkg Installing /packages/All/suitesparse-colamd-3.0.3_1.pkg Installing /packages/All/suitesparse-ccolamd-3.0.3_1.pkg Installing /packages/All/suitesparse-cholmod-4.0.3_1.pkg Installing /packages/All/suitesparse-umfpack-6.1.0_1.pkg Installing /packages/All/libffi-3.4.4.pkg Installing /packages/All/expat-2.5.0.pkg Installing /packages/All/mpdecimal-2.5.1.pkg Installing /packages/All/ncurses-6.4.pkg ===== Message from ncurses-6.4: -- To get the terminfo database please install the terminfo-db package: pkg install terminfo-db Installing /packages/All/readline-8.2.1.pkg Installing /packages/All/openssl-1.1.1u,1.pkg Installing /packages/All/python39-3.9.17.pkg ===== Message from python39-3.9.17: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 Installing /packages/All/py39-setuptools-63.1.0_1.pkg Installing /packages/All/py39-numpy-1.24.1_4,1.pkg Installing /packages/All/py39-cython-0.29.35.pkg Installing /packages/All/ccache-3.7.12_4.pkg Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for gcc create symlink for gcc (world) create symlink for g++ create symlink for g++ (world) create symlink for gcc12 create symlink for gcc12 (world) create symlink for g++12 create symlink for g++12 (world) create symlink for cpp12 create symlink for cpp12 (world) ===== Message from ccache-3.7.12_4: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. UNFLAVORED devel/binutils -> use devel/binutils@native SUCCEEDED 00:00:09 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> py39-bx-python-0.8.13_1 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> py39-bx-python-0.8.13_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-bx-python-0.8.13_1 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> py39-bx-python-0.8.13_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-bx-python-0.8.13_1 for building => SHA256 Checksum OK for bx-python-0.8.13.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> py39-bx-python-0.8.13_1 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-bx-python-0.8.13_1 for building ===> Extracting for py39-bx-python-0.8.13_1 => SHA256 Checksum OK for bx-python-0.8.13.tar.gz. Extracted Memory Use: 9.71M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for py39-bx-python-0.8.13_1 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> py39-bx-python-0.8.13_1 depends on package: py39-numpy>=1.16,1<1.25,1 - found ===> py39-bx-python-0.8.13_1 depends on executable: cython-3.9 - found ===> py39-bx-python-0.8.13_1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-bx-python-0.8.13_1 depends on file: /usr/local/bin/python3.9 - found ===> py39-bx-python-0.8.13_1 depends on file: /usr/local/bin/ccache - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> py39-bx-python-0.8.13_1 depends on package: py39-numpy>=1.16,1<1.25,1 - found ===> py39-bx-python-0.8.13_1 depends on executable: cython-3.9 - found ===> py39-bx-python-0.8.13_1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-bx-python-0.8.13_1 depends on file: /usr/local/bin/python3.9 - found ===> py39-bx-python-0.8.13_1 depends on file: /usr/local/bin/ccache - found ===> Configuring for py39-bx-python-0.8.13_1 running config SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for py39-bx-python-0.8.13_1 running build running build_py creating build creating build/lib.dragonfly-6.5-x86_64-cpython-39 copying lib/psyco_full.py -> build/lib.dragonfly-6.5-x86_64-cpython-39 creating build/lib.dragonfly-6.5-x86_64-cpython-39/bx copying lib/bx/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx copying lib/bx/binned_array.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx copying lib/bx/binned_array_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx copying lib/bx/bitset_builders.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx copying lib/bx/bitset_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx copying lib/bx/bitset_utils.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx copying lib/bx/filter.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx copying lib/bx/gene_reader.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx copying lib/bx/interval_index_file.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx copying lib/bx/interval_index_file_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx copying lib/bx/seqmapping.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx copying lib/bx/seqmapping_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx copying lib/bx/wiggle.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx copying lib/bx/wiggle_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx creating build/lib.dragonfly-6.5-x86_64-cpython-39/bx_extras copying lib/bx_extras/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx_extras copying lib/bx_extras/fpconst.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx_extras copying lib/bx_extras/fpconst_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx_extras copying lib/bx_extras/lrucache.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx_extras copying lib/bx_extras/pstat.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx_extras copying lib/bx_extras/pyparsing.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx_extras copying lib/bx_extras/stats.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx_extras creating build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align copying lib/bx/align/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align copying lib/bx/align/axt.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align copying lib/bx/align/core.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align copying lib/bx/align/epo.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align copying lib/bx/align/epo_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align copying lib/bx/align/lav.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align copying lib/bx/align/lav_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align copying lib/bx/align/maf.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align copying lib/bx/align/maf_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align copying lib/bx/align/score.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align copying lib/bx/align/score_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align creating build/lib.dragonfly-6.5-x86_64-cpython-39/bx/arrays copying lib/bx/arrays/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/arrays copying lib/bx/arrays/array_tree_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/arrays creating build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bbi copying lib/bx/bbi/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bbi copying lib/bx/bbi/bigwig_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bbi creating build/lib.dragonfly-6.5-x86_64-cpython-39/bx/cookbook copying lib/bx/cookbook/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/cookbook copying lib/bx/cookbook/argparse.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/cookbook copying lib/bx/cookbook/attribute.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/cookbook copying lib/bx/cookbook/doc_optparse.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/cookbook copying lib/bx/cookbook/progress_bar.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/cookbook creating build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals copying lib/bx/intervals/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals copying lib/bx/intervals/cluster_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals copying lib/bx/intervals/intersection_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals copying lib/bx/intervals/io.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals copying lib/bx/intervals/random_intervals.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals creating build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intseq copying lib/bx/intseq/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intseq creating build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc copying lib/bx/misc/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc copying lib/bx/misc/bgzf_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc copying lib/bx/misc/binary_file.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc copying lib/bx/misc/cdb.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc copying lib/bx/misc/cdb_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc copying lib/bx/misc/filecache.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc copying lib/bx/misc/filecache_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc copying lib/bx/misc/readlengths.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc copying lib/bx/misc/seekbzip2.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc copying lib/bx/misc/seekbzip2_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc copying lib/bx/misc/seeklzop.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc copying lib/bx/misc/seeklzop_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc creating build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif copying lib/bx/motif/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif copying lib/bx/motif/pwm.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif copying lib/bx/motif/pwm_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif creating build/lib.dragonfly-6.5-x86_64-cpython-39/bx/phylo copying lib/bx/phylo/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/phylo copying lib/bx/phylo/newick.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/phylo copying lib/bx/phylo/newick_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/phylo copying lib/bx/phylo/phast.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/phylo copying lib/bx/phylo/phast_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/phylo creating build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm copying lib/bx/pwm/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm copying lib/bx/pwm/bed_score_aligned_pwm.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm copying lib/bx/pwm/bed_score_aligned_string.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm copying lib/bx/pwm/maf_select_motifs.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm copying lib/bx/pwm/position_weight_matrix.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm copying lib/bx/pwm/pwm_score_maf.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm copying lib/bx/pwm/pwm_score_motifs.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm copying lib/bx/pwm/pwm_score_positions.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm copying lib/bx/pwm/pwm_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm creating build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq copying lib/bx/seq/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq copying lib/bx/seq/core.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq copying lib/bx/seq/fasta.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq copying lib/bx/seq/fasta_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq copying lib/bx/seq/nib.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq copying lib/bx/seq/nib_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq copying lib/bx/seq/qdna.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq copying lib/bx/seq/qdna_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq copying lib/bx/seq/seq.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq copying lib/bx/seq/seq_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq copying lib/bx/seq/twobit.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq copying lib/bx/seq/twobit_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq creating build/lib.dragonfly-6.5-x86_64-cpython-39/bx/tabular copying lib/bx/tabular/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/tabular copying lib/bx/tabular/io.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/tabular creating build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/sitemask copying lib/bx/align/sitemask/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/sitemask copying lib/bx/align/sitemask/core.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/sitemask copying lib/bx/align/sitemask/cpg.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/sitemask copying lib/bx/align/sitemask/quality.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/sitemask copying lib/bx/align/sitemask/sitemask_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/sitemask creating build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/tools copying lib/bx/align/tools/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/tools copying lib/bx/align/tools/chop.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/tools copying lib/bx/align/tools/fuse.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/tools copying lib/bx/align/tools/thread.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/tools copying lib/bx/align/tools/tile.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/tools creating build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/base_coverage.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/complement.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/concat.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/coverage.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/find_clusters.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/intersect.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/join.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/merge.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/quicksect.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations copying lib/bx/intervals/operations/subtract.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations creating build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif/io copying lib/bx/motif/io/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif/io copying lib/bx/motif/io/transfac.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif/io copying lib/bx/motif/io/transfac_tests.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif/io creating build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif/logo copying lib/bx/motif/logo/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif/logo copying lib/bx/motif/logo/template.ps -> build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif/logo running build_ext skipping 'lib/bx/bitset.c' Cython extension (up-to-date) skipping 'lib/bx/intervals/intersection.c' Cython extension (up-to-date) skipping 'lib/bx/align/_core.c' Cython extension (up-to-date) skipping 'lib/bx/seq/_nib.c' Cython extension (up-to-date) skipping 'lib/bx/seq/_twobit.c' Cython extension (up-to-date) skipping 'lib/bx/_seqmapping.c' Cython extension (up-to-date) skipping 'lib/bx/misc/bgzf.c' Cython extension (up-to-date) skipping 'lib/bx/intervals/cluster.c' Cython extension (up-to-date) skipping 'lib/bx/pwm/_position_weight_matrix.c' Cython extension (up-to-date) skipping 'lib/bx/motif/_pwm.c' Cython extension (up-to-date) skipping 'lib/bx/arrays/array_tree.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bpt_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/cirtree_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bbi_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bigwig_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bigbed_file.c' Cython extension (up-to-date) skipping 'lib/bx/align/_epo.c' Cython extension (up-to-date) skipping 'lib/bx/arrays/bed.c' Cython extension (up-to-date) skipping 'lib/bx/arrays/wiggle.c' Cython extension (up-to-date) skipping 'lib/bx/align/sitemask/_cpg.c' Cython extension (up-to-date) skipping 'lib/bx/intseq/ngramcount.c' Cython extension (up-to-date) skipping 'lib/bx/misc/_seekbzip2.c' Cython extension (up-to-date) building 'bx.bitset' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39 creating build/temp.dragonfly-6.5-x86_64-cpython-39/lib creating build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx creating build/temp.dragonfly-6.5-x86_64-cpython-39/src creating build/temp.dragonfly-6.5-x86_64-cpython-39/src/kent cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc/kent -Isrc -I/usr/local/include/python3.9 -c lib/bx/bitset.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/bitset.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc/kent -Isrc -I/usr/local/include/python3.9 -c src/binBits.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/src/binBits.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc/kent -Isrc -I/usr/local/include/python3.9 -c src/kent/bits.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/src/kent/bits.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc/kent -Isrc -I/usr/local/include/python3.9 -c src/kent/common.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/src/kent/common.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/bitset.o build/temp.dragonfly-6.5-x86_64-cpython-39/src/binBits.o build/temp.dragonfly-6.5-x86_64-cpython-39/src/kent/bits.o build/temp.dragonfly-6.5-x86_64-cpython-39/src/kent/common.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bitset.cpython-39.so building 'bx.intervals.intersection' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/intervals cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -c lib/bx/intervals/intersection.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/intervals/intersection.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/intervals/intersection.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/intersection.cpython-39.so building 'bx.align._core' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/align cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -c lib/bx/align/_core.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/align/_core.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/align/_core.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/_core.cpython-39.so building 'bx.seq._nib' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/seq cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -c lib/bx/seq/_nib.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/seq/_nib.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/seq/_nib.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq/_nib.cpython-39.so building 'bx.seq._twobit' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -c lib/bx/seq/_twobit.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/seq/_twobit.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/seq/_twobit.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq/_twobit.cpython-39.so building 'bx._seqmapping' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -c lib/bx/_seqmapping.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/_seqmapping.o lib/bx/_seqmapping.c: In function '__pyx_pf_2bx_11_seqmapping_21CharToIntArrayMapping_6translate': lib/bx/_seqmapping.c:1876:3: warning: 'PyObject_AsWriteBuffer' is deprecated [-Wdeprecated-declarations] __pyx_t_1 = PyObject_AsWriteBuffer(__pyx_v_rval, ((void **)(&__pyx_v_t_buf)), (&__pyx_v_t_len)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 52, __pyx_L1_error) ^~~~~~~~~ In file included from /usr/local/include/python3.9/Python.h:146, from lib/bx/_seqmapping.c:6: /usr/local/include/python3.9/abstract.h:354:17: note: declared here PyAPI_FUNC(int) PyObject_AsWriteBuffer(PyObject *obj, ^~~~~~~~~~~~~~~~~~~~~~ lib/bx/_seqmapping.c: In function '__pyx_pf_2bx_11_seqmapping_21CharToIntArrayMapping_8translate_list': lib/bx/_seqmapping.c:2079:3: warning: 'PyObject_AsWriteBuffer' is deprecated [-Wdeprecated-declarations] __pyx_t_7 = PyObject_AsWriteBuffer(__pyx_v_rval, ((void **)(&__pyx_v_t_buf)), (&__pyx_v_t_len)); if (unlikely(__pyx_t_7 == ((int)-1))) __PYX_ERR(0, 75, __pyx_L1_error) ^~~~~~~~~ In file included from /usr/local/include/python3.9/Python.h:146, from lib/bx/_seqmapping.c:6: /usr/local/include/python3.9/abstract.h:354:17: note: declared here PyAPI_FUNC(int) PyObject_AsWriteBuffer(PyObject *obj, ^~~~~~~~~~~~~~~~~~~~~~ lib/bx/_seqmapping.c: In function '__pyx_pf_2bx_11_seqmapping_15IntToIntMapping_6translate': lib/bx/_seqmapping.c:3154:3: warning: 'PyObject_AsReadBuffer' is deprecated [-Wdeprecated-declarations] __pyx_t_1 = PyObject_AsReadBuffer(__pyx_v_src, ((void const **)(&__pyx_v_s_buf)), (&__pyx_v_s_len)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 132, __pyx_L1_error) ^~~~~~~~~ In file included from /usr/local/include/python3.9/Python.h:146, from lib/bx/_seqmapping.c:6: /usr/local/include/python3.9/abstract.h:343:17: note: declared here PyAPI_FUNC(int) PyObject_AsReadBuffer(PyObject *obj, ^~~~~~~~~~~~~~~~~~~~~ lib/bx/_seqmapping.c:3255:3: warning: 'PyObject_AsWriteBuffer' is deprecated [-Wdeprecated-declarations] __pyx_t_1 = PyObject_AsWriteBuffer(__pyx_v_rval, ((void **)(&__pyx_v_t_buf)), (&__pyx_v_t_len)); if (unlikely(__pyx_t_1 == ((int)-1))) __PYX_ERR(0, 137, __pyx_L1_error) ^~~~~~~~~ In file included from /usr/local/include/python3.9/Python.h:146, from lib/bx/_seqmapping.c:6: /usr/local/include/python3.9/abstract.h:354:17: note: declared here PyAPI_FUNC(int) PyObject_AsWriteBuffer(PyObject *obj, ^~~~~~~~~~~~~~~~~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/_seqmapping.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/_seqmapping.cpython-39.so building 'bx.misc.bgzf' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/misc creating build/temp.dragonfly-6.5-x86_64-cpython-39/src/samtools cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc/samtools -I/usr/local/include/python3.9 -c lib/bx/misc/bgzf.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/misc/bgzf.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc/samtools -I/usr/local/include/python3.9 -c src/samtools/bgzf.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/src/samtools/bgzf.o src/samtools/bgzf.c: In function 'cache_block': src/samtools/bgzf.c:422:40: warning: comparison of integer expressions of different signedness: 'khint_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] if ((kh_size(h) + 1) * MAX_BLOCK_SIZE > fp->cache_size) { ^ src/samtools/bgzf.c: In function 'read_block': src/samtools/bgzf.c:462:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] if (count != sizeof(header)) { ^~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/misc/bgzf.o build/temp.dragonfly-6.5-x86_64-cpython-39/src/samtools/bgzf.o -L/usr/local/lib -lz -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc/bgzf.cpython-39.so building 'bx.intervals.cluster' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.9 -c lib/bx/intervals/cluster.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/intervals/cluster.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.9 -c src/cluster.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/src/cluster.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/intervals/cluster.o build/temp.dragonfly-6.5-x86_64-cpython-39/src/cluster.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/cluster.cpython-39.so building 'bx.pwm._position_weight_matrix' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/pwm cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.9 -c lib/bx/pwm/_position_weight_matrix.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/pwm/_position_weight_matrix.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.9 -c src/pwm_utils.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/src/pwm_utils.o src/pwm_utils.c: In function 'main': src/pwm_utils.c:11:27: warning: implicit declaration of function 'strlen' [-Wimplicit-function-declaration] int string_size = strlen(argv[1]); ^~~~~~ src/pwm_utils.c:11:27: warning: incompatible implicit declaration of built-in function 'strlen' src/pwm_utils.c:11:27: note: include '' or provide a declaration of 'strlen' src/pwm_utils.c:5:1: +#include src/pwm_utils.c:11:27: int string_size = strlen(argv[1]); ^~~~~~ src/pwm_utils.c:12:29: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare] if (strlen(argv[2]) != string_size) { ^~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/pwm/_position_weight_matrix.o build/temp.dragonfly-6.5-x86_64-cpython-39/src/pwm_utils.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm/_position_weight_matrix.cpython-39.so building 'bx.motif._pwm' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/motif cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c lib/bx/motif/_pwm.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/motif/_pwm.o In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, from lib/bx/motif/_pwm.c:679: /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/motif/_pwm.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif/_pwm.cpython-39.so building 'bx.arrays.array_tree' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/arrays cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c lib/bx/arrays/array_tree.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/arrays/array_tree.o In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, from lib/bx/arrays/array_tree.c:681: /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/arrays/array_tree.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/arrays/array_tree.cpython-39.so building 'bx.bbi.bpt_file' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/bbi cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -c lib/bx/bbi/bpt_file.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/bbi/bpt_file.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/bbi/bpt_file.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bbi/bpt_file.cpython-39.so building 'bx.bbi.cirtree_file' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -c lib/bx/bbi/cirtree_file.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/bbi/cirtree_file.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/bbi/cirtree_file.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bbi/cirtree_file.cpython-39.so building 'bx.bbi.bbi_file' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c lib/bx/bbi/bbi_file.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/bbi/bbi_file.o In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, from lib/bx/bbi/bbi_file.c:681: /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/bbi/bbi_file.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bbi/bbi_file.cpython-39.so building 'bx.bbi.bigwig_file' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c lib/bx/bbi/bigwig_file.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/bbi/bigwig_file.o In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, from lib/bx/bbi/bigwig_file.c:681: /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ lib/bx/bbi/bigwig_file.c: In function '__pyx_f_2bx_3bbi_11bigwig_file_18BigWigBlockHandler_handle_block': lib/bx/bbi/bigwig_file.c:3351:30: warning: comparison of integer expressions of different signedness: 'int' and '__pyx_t_2bx_3bbi_5types_bits32' {aka 'unsigned int'} [-Wsign-compare] __pyx_t_11 = ((__pyx_v_s < __pyx_v_self->start) != 0); ^ lib/bx/bbi/bigwig_file.c:3380:30: warning: comparison of integer expressions of different signedness: 'int' and '__pyx_t_2bx_3bbi_5types_bits32' {aka 'unsigned int'} [-Wsign-compare] __pyx_t_11 = ((__pyx_v_e > __pyx_v_self->end) != 0); ^ lib/bx/bbi/bigwig_file.c: In function '__pyx_f_2bx_3bbi_11bigwig_file_29ArrayAccumulatingBlockHandler_handle_interval_value': lib/bx/bbi/bigwig_file.c:5304:76: warning: comparison of integer expressions of different signedness: 'int' and '__pyx_t_2bx_3bbi_5types_bits32' {aka 'unsigned int'} [-Wsign-compare] for (__pyx_v_i = (__pyx_v_s - __pyx_v_self->__pyx_base.start); __pyx_v_i < __pyx_t_2; __pyx_v_i++) { ^ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/bbi/bigwig_file.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bbi/bigwig_file.cpython-39.so building 'bx.bbi.bigbed_file' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c lib/bx/bbi/bigbed_file.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/bbi/bigbed_file.o In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, from lib/bx/bbi/bigbed_file.c:681: /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/bbi/bigbed_file.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bbi/bigbed_file.cpython-39.so building 'bx.align._epo' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include/python3.9 -c lib/bx/align/_epo.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/align/_epo.o In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1940, from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5, from lib/bx/align/_epo.c:681: /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ lib/bx/align/_epo.c: In function '__pyx_f_2bx_5align_4_epo_bed_union': lib/bx/align/_epo.c:5472:237: warning: comparison of integer expressions of different signedness: '__pyx_t_5numpy_uint64_t' {aka 'long unsigned int'} and 'Py_ssize_t' {aka 'long int'} [-Wsign-compare] __pyx_t_4 = (((*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_uint64_t *, __pyx_pybuffernd_elements.rcbuffer->pybuffer.buf, __pyx_t_11, __pyx_pybuffernd_elements.diminfo[0].strides, __pyx_t_12, __pyx_pybuffernd_elements.diminfo[1].strides)) <= __pyx_v_cen) != 0); ^~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/align/_epo.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/_epo.cpython-39.so building 'bx.arrays.bed' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -c lib/bx/arrays/bed.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/arrays/bed.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/arrays/bed.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/arrays/bed.cpython-39.so building 'bx.arrays.wiggle' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -c lib/bx/arrays/wiggle.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/arrays/wiggle.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/arrays/wiggle.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/arrays/wiggle.cpython-39.so building 'bx.align.sitemask._cpg' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/align/sitemask cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -c lib/bx/align/sitemask/_cpg.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/align/sitemask/_cpg.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -c lib/bx/align/sitemask/find_cpg.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/align/sitemask/find_cpg.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/align/sitemask/_cpg.o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/align/sitemask/find_cpg.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/sitemask/_cpg.cpython-39.so building 'bx.intseq.ngramcount' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/intseq cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc -I/usr/local/include/python3.9 -c lib/bx/intseq/ngramcount.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/intseq/ngramcount.o cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/intseq/ngramcount.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intseq/ngramcount.cpython-39.so building 'bx.misc._seekbzip2' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39/src/bunzip cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc/bunzip -I/usr/local/include/python3.9 -c lib/bx/misc/_seekbzip2.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/misc/_seekbzip2.o cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -Isrc/bunzip -I/usr/local/include/python3.9 -c src/bunzip/micro-bunzip.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/src/bunzip/micro-bunzip.o src/bunzip/micro-bunzip.c: In function 'get_bits': src/bunzip/micro-bunzip.c:99:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'char' [-Wsign-compare] while (bd->inbufBitCount dbufSize) return RETVAL_DATA_ERROR; ^ src/bunzip/micro-bunzip.c:298:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] while (bd->inbufBitCountmaxLen) { ^ src/bunzip/micro-bunzip.c:400:13: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] if(origPtr>=dbufCount) return RETVAL_DATA_ERROR; ^~ cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/lib/bx/misc/_seekbzip2.o build/temp.dragonfly-6.5-x86_64-cpython-39/src/bunzip/micro-bunzip.o -L/usr/local/lib -o build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc/_seekbzip2.cpython-39.so running build_scripts creating build/scripts-3.9 copying and adjusting scripts/aggregate_scores_in_intervals.py -> build/scripts-3.9 copying and adjusting scripts/align_print_template.py -> build/scripts-3.9 copying and adjusting scripts/axt_extract_ranges.py -> build/scripts-3.9 copying and adjusting scripts/axt_to_fasta.py -> build/scripts-3.9 copying and adjusting scripts/axt_to_lav.py -> build/scripts-3.9 copying and adjusting scripts/axt_to_maf.py -> build/scripts-3.9 copying and adjusting scripts/bed_bigwig_profile.py -> build/scripts-3.9 copying and adjusting scripts/bed_build_windows.py -> build/scripts-3.9 copying and adjusting scripts/bed_complement.py -> build/scripts-3.9 copying and adjusting scripts/bed_count_by_interval.py -> build/scripts-3.9 copying and adjusting scripts/bed_count_overlapping.py -> build/scripts-3.9 copying and adjusting scripts/bed_coverage.py -> build/scripts-3.9 copying and adjusting scripts/bed_coverage_by_interval.py -> build/scripts-3.9 copying and adjusting scripts/bed_diff_basewise_summary.py -> build/scripts-3.9 copying and adjusting scripts/bed_extend_to.py -> build/scripts-3.9 copying and adjusting scripts/bed_intersect.py -> build/scripts-3.9 copying and adjusting scripts/bed_intersect_basewise.py -> build/scripts-3.9 copying and adjusting scripts/bed_merge_overlapping.py -> build/scripts-3.9 copying and adjusting scripts/bed_rand_intersect.py -> build/scripts-3.9 copying and adjusting scripts/bed_subtract_basewise.py -> build/scripts-3.9 copying and adjusting scripts/bnMapper.py -> build/scripts-3.9 copying and adjusting scripts/div_snp_table_chr.py -> build/scripts-3.9 copying and adjusting scripts/find_in_sorted_file.py -> build/scripts-3.9 copying and adjusting scripts/gene_fourfold_sites.py -> build/scripts-3.9 copying and adjusting scripts/get_scores_in_intervals.py -> build/scripts-3.9 copying and adjusting scripts/int_seqs_to_char_strings.py -> build/scripts-3.9 copying and adjusting scripts/interval_count_intersections.py -> build/scripts-3.9 copying and adjusting scripts/interval_join.py -> build/scripts-3.9 copying and adjusting scripts/lav_to_axt.py -> build/scripts-3.9 copying and adjusting scripts/lav_to_maf.py -> build/scripts-3.9 copying and adjusting scripts/line_select.py -> build/scripts-3.9 copying and adjusting scripts/lzop_build_offset_table.py -> build/scripts-3.9 copying and adjusting scripts/mMK_bitset.py -> build/scripts-3.9 copying and adjusting scripts/maf_build_index.py -> build/scripts-3.9 copying and adjusting scripts/maf_chop.py -> build/scripts-3.9 copying and adjusting scripts/maf_chunk.py -> build/scripts-3.9 copying and adjusting scripts/maf_col_counts.py -> build/scripts-3.9 copying and adjusting scripts/maf_col_counts_all.py -> build/scripts-3.9 copying and adjusting scripts/maf_count.py -> build/scripts-3.9 copying and adjusting scripts/maf_covered_ranges.py -> build/scripts-3.9 copying and adjusting scripts/maf_covered_regions.py -> build/scripts-3.9 copying and adjusting scripts/maf_div_sites.py -> build/scripts-3.9 copying and adjusting scripts/maf_drop_overlapping.py -> build/scripts-3.9 copying and adjusting scripts/maf_extract_chrom_ranges.py -> build/scripts-3.9 copying and adjusting scripts/maf_extract_ranges.py -> build/scripts-3.9 copying and adjusting scripts/maf_extract_ranges_indexed.py -> build/scripts-3.9 copying and adjusting scripts/maf_filter.py -> build/scripts-3.9 copying and adjusting scripts/maf_filter_max_wc.py -> build/scripts-3.9 copying and adjusting scripts/maf_gap_frequency.py -> build/scripts-3.9 copying and adjusting scripts/maf_gc_content.py -> build/scripts-3.9 copying and adjusting scripts/maf_interval_alignibility.py -> build/scripts-3.9 copying and adjusting scripts/maf_limit_to_species.py -> build/scripts-3.9 copying and adjusting scripts/maf_mapping_word_frequency.py -> build/scripts-3.9 copying and adjusting scripts/maf_mask_cpg.py -> build/scripts-3.9 copying and adjusting scripts/maf_mean_length_ungapped_piece.py -> build/scripts-3.9 copying and adjusting scripts/maf_percent_columns_matching.py -> build/scripts-3.9 copying and adjusting scripts/maf_percent_identity.py -> build/scripts-3.9 copying and adjusting scripts/maf_print_chroms.py -> build/scripts-3.9 copying and adjusting scripts/maf_print_scores.py -> build/scripts-3.9 copying and adjusting scripts/maf_randomize.py -> build/scripts-3.9 copying and adjusting scripts/maf_region_coverage_by_src.py -> build/scripts-3.9 copying and adjusting scripts/maf_select.py -> build/scripts-3.9 copying and adjusting scripts/maf_shuffle_columns.py -> build/scripts-3.9 copying and adjusting scripts/maf_species_in_all_files.py -> build/scripts-3.9 copying and adjusting scripts/maf_split_by_src.py -> build/scripts-3.9 copying and adjusting scripts/maf_thread_for_species.py -> build/scripts-3.9 copying and adjusting scripts/maf_tile.py -> build/scripts-3.9 copying and adjusting scripts/maf_tile_2.py -> build/scripts-3.9 copying and adjusting scripts/maf_tile_2bit.py -> build/scripts-3.9 copying and adjusting scripts/maf_to_axt.py -> build/scripts-3.9 copying and adjusting scripts/maf_to_concat_fasta.py -> build/scripts-3.9 copying and adjusting scripts/maf_to_fasta.py -> build/scripts-3.9 copying and adjusting scripts/maf_to_int_seqs.py -> build/scripts-3.9 copying and adjusting scripts/maf_translate_chars.py -> build/scripts-3.9 copying and adjusting scripts/maf_truncate.py -> build/scripts-3.9 copying and adjusting scripts/maf_word_frequency.py -> build/scripts-3.9 copying and adjusting scripts/mask_quality.py -> build/scripts-3.9 copying and adjusting scripts/nib_chrom_intervals_to_fasta.py -> build/scripts-3.9 copying and adjusting scripts/nib_intervals_to_fasta.py -> build/scripts-3.9 copying and adjusting scripts/nib_length.py -> build/scripts-3.9 copying and adjusting scripts/one_field_per_line.py -> build/scripts-3.9 copying and adjusting scripts/out_to_chain.py -> build/scripts-3.9 copying and adjusting scripts/prefix_lines.py -> build/scripts-3.9 copying and adjusting scripts/pretty_table.py -> build/scripts-3.9 copying and adjusting scripts/qv_to_bqv.py -> build/scripts-3.9 copying and adjusting scripts/random_lines.py -> build/scripts-3.9 copying and adjusting scripts/table_add_column.py -> build/scripts-3.9 copying and adjusting scripts/table_filter.py -> build/scripts-3.9 copying and adjusting scripts/tfloc_summary.py -> build/scripts-3.9 copying and adjusting scripts/ucsc_gene_table_to_intervals.py -> build/scripts-3.9 copying and adjusting scripts/wiggle_to_array_tree.py -> build/scripts-3.9 copying and adjusting scripts/wiggle_to_binned_array.py -> build/scripts-3.9 copying and adjusting scripts/wiggle_to_chr_binned_array.py -> build/scripts-3.9 copying and adjusting scripts/wiggle_to_simple.py -> build/scripts-3.9 changing mode of build/scripts-3.9/aggregate_scores_in_intervals.py from 644 to 755 changing mode of build/scripts-3.9/align_print_template.py from 644 to 755 changing mode of build/scripts-3.9/axt_extract_ranges.py from 644 to 755 changing mode of build/scripts-3.9/axt_to_fasta.py from 644 to 755 changing mode of build/scripts-3.9/axt_to_lav.py from 644 to 755 changing mode of build/scripts-3.9/axt_to_maf.py from 644 to 755 changing mode of build/scripts-3.9/bed_bigwig_profile.py from 644 to 755 changing mode of build/scripts-3.9/bed_build_windows.py from 644 to 755 changing mode of build/scripts-3.9/bed_complement.py from 644 to 755 changing mode of build/scripts-3.9/bed_count_by_interval.py from 644 to 755 changing mode of build/scripts-3.9/bed_count_overlapping.py from 644 to 755 changing mode of build/scripts-3.9/bed_coverage.py from 644 to 755 changing mode of build/scripts-3.9/bed_coverage_by_interval.py from 644 to 755 changing mode of build/scripts-3.9/bed_diff_basewise_summary.py from 644 to 755 changing mode of build/scripts-3.9/bed_extend_to.py from 644 to 755 changing mode of build/scripts-3.9/bed_intersect.py from 644 to 755 changing mode of build/scripts-3.9/bed_intersect_basewise.py from 644 to 755 changing mode of build/scripts-3.9/bed_merge_overlapping.py from 644 to 755 changing mode of build/scripts-3.9/bed_rand_intersect.py from 644 to 755 changing mode of build/scripts-3.9/bed_subtract_basewise.py from 644 to 755 changing mode of build/scripts-3.9/bnMapper.py from 644 to 755 changing mode of build/scripts-3.9/div_snp_table_chr.py from 644 to 755 changing mode of build/scripts-3.9/find_in_sorted_file.py from 644 to 755 changing mode of build/scripts-3.9/gene_fourfold_sites.py from 644 to 755 changing mode of build/scripts-3.9/get_scores_in_intervals.py from 644 to 755 changing mode of build/scripts-3.9/int_seqs_to_char_strings.py from 644 to 755 changing mode of build/scripts-3.9/interval_count_intersections.py from 644 to 755 changing mode of build/scripts-3.9/interval_join.py from 644 to 755 changing mode of build/scripts-3.9/lav_to_axt.py from 644 to 755 changing mode of build/scripts-3.9/lav_to_maf.py from 644 to 755 changing mode of build/scripts-3.9/line_select.py from 644 to 755 changing mode of build/scripts-3.9/lzop_build_offset_table.py from 644 to 755 changing mode of build/scripts-3.9/mMK_bitset.py from 644 to 755 changing mode of build/scripts-3.9/maf_build_index.py from 644 to 755 changing mode of build/scripts-3.9/maf_chop.py from 644 to 755 changing mode of build/scripts-3.9/maf_chunk.py from 644 to 755 changing mode of build/scripts-3.9/maf_col_counts.py from 644 to 755 changing mode of build/scripts-3.9/maf_col_counts_all.py from 644 to 755 changing mode of build/scripts-3.9/maf_count.py from 644 to 755 changing mode of build/scripts-3.9/maf_covered_ranges.py from 644 to 755 changing mode of build/scripts-3.9/maf_covered_regions.py from 644 to 755 changing mode of build/scripts-3.9/maf_div_sites.py from 644 to 755 changing mode of build/scripts-3.9/maf_drop_overlapping.py from 644 to 755 changing mode of build/scripts-3.9/maf_extract_chrom_ranges.py from 644 to 755 changing mode of build/scripts-3.9/maf_extract_ranges.py from 644 to 755 changing mode of build/scripts-3.9/maf_extract_ranges_indexed.py from 644 to 755 changing mode of build/scripts-3.9/maf_filter.py from 644 to 755 changing mode of build/scripts-3.9/maf_filter_max_wc.py from 644 to 755 changing mode of build/scripts-3.9/maf_gap_frequency.py from 644 to 755 changing mode of build/scripts-3.9/maf_gc_content.py from 644 to 755 changing mode of build/scripts-3.9/maf_interval_alignibility.py from 644 to 755 changing mode of build/scripts-3.9/maf_limit_to_species.py from 644 to 755 changing mode of build/scripts-3.9/maf_mapping_word_frequency.py from 644 to 755 changing mode of build/scripts-3.9/maf_mask_cpg.py from 644 to 755 changing mode of build/scripts-3.9/maf_mean_length_ungapped_piece.py from 644 to 755 changing mode of build/scripts-3.9/maf_percent_columns_matching.py from 644 to 755 changing mode of build/scripts-3.9/maf_percent_identity.py from 644 to 755 changing mode of build/scripts-3.9/maf_print_chroms.py from 644 to 755 changing mode of build/scripts-3.9/maf_print_scores.py from 644 to 755 changing mode of build/scripts-3.9/maf_randomize.py from 644 to 755 changing mode of build/scripts-3.9/maf_region_coverage_by_src.py from 644 to 755 changing mode of build/scripts-3.9/maf_select.py from 644 to 755 changing mode of build/scripts-3.9/maf_shuffle_columns.py from 644 to 755 changing mode of build/scripts-3.9/maf_species_in_all_files.py from 644 to 755 changing mode of build/scripts-3.9/maf_split_by_src.py from 644 to 755 changing mode of build/scripts-3.9/maf_thread_for_species.py from 644 to 755 changing mode of build/scripts-3.9/maf_tile.py from 644 to 755 changing mode of build/scripts-3.9/maf_tile_2.py from 644 to 755 changing mode of build/scripts-3.9/maf_tile_2bit.py from 644 to 755 changing mode of build/scripts-3.9/maf_to_axt.py from 644 to 755 changing mode of build/scripts-3.9/maf_to_concat_fasta.py from 644 to 755 changing mode of build/scripts-3.9/maf_to_fasta.py from 644 to 755 changing mode of build/scripts-3.9/maf_to_int_seqs.py from 644 to 755 changing mode of build/scripts-3.9/maf_translate_chars.py from 644 to 755 changing mode of build/scripts-3.9/maf_truncate.py from 644 to 755 changing mode of build/scripts-3.9/maf_word_frequency.py from 644 to 755 changing mode of build/scripts-3.9/mask_quality.py from 644 to 755 changing mode of build/scripts-3.9/nib_chrom_intervals_to_fasta.py from 644 to 755 changing mode of build/scripts-3.9/nib_intervals_to_fasta.py from 644 to 755 changing mode of build/scripts-3.9/nib_length.py from 644 to 755 changing mode of build/scripts-3.9/one_field_per_line.py from 644 to 755 changing mode of build/scripts-3.9/out_to_chain.py from 644 to 755 changing mode of build/scripts-3.9/prefix_lines.py from 644 to 755 changing mode of build/scripts-3.9/pretty_table.py from 644 to 755 changing mode of build/scripts-3.9/qv_to_bqv.py from 644 to 755 changing mode of build/scripts-3.9/random_lines.py from 644 to 755 changing mode of build/scripts-3.9/table_add_column.py from 644 to 755 changing mode of build/scripts-3.9/table_filter.py from 644 to 755 changing mode of build/scripts-3.9/tfloc_summary.py from 644 to 755 changing mode of build/scripts-3.9/ucsc_gene_table_to_intervals.py from 644 to 755 changing mode of build/scripts-3.9/wiggle_to_array_tree.py from 644 to 755 changing mode of build/scripts-3.9/wiggle_to_binned_array.py from 644 to 755 changing mode of build/scripts-3.9/wiggle_to_chr_binned_array.py from 644 to 755 changing mode of build/scripts-3.9/wiggle_to_simple.py from 644 to 755 SUCCEEDED 00:01:40 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> py39-bx-python-0.8.13_1 depends on package: py39-numpy>=1.16,1<1.25,1 - found ===> py39-bx-python-0.8.13_1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-bx-python-0.8.13_1 depends on file: /usr/local/bin/python3.9 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for py39-bx-python-0.8.13_1 ===> py39-bx-python-0.8.13_1 depends on package: py39-numpy>=1.16,1<1.25,1 - found ===> py39-bx-python-0.8.13_1 depends on package: py39-setuptools>=63.1.0 - found ===> py39-bx-python-0.8.13_1 depends on file: /usr/local/bin/python3.9 - found ===> Generating temporary packing list running install /usr/local/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running build_ext skipping 'lib/bx/bitset.c' Cython extension (up-to-date) skipping 'lib/bx/intervals/intersection.c' Cython extension (up-to-date) skipping 'lib/bx/align/_core.c' Cython extension (up-to-date) skipping 'lib/bx/seq/_nib.c' Cython extension (up-to-date) skipping 'lib/bx/seq/_twobit.c' Cython extension (up-to-date) skipping 'lib/bx/_seqmapping.c' Cython extension (up-to-date) skipping 'lib/bx/misc/bgzf.c' Cython extension (up-to-date) skipping 'lib/bx/intervals/cluster.c' Cython extension (up-to-date) skipping 'lib/bx/pwm/_position_weight_matrix.c' Cython extension (up-to-date) skipping 'lib/bx/motif/_pwm.c' Cython extension (up-to-date) skipping 'lib/bx/arrays/array_tree.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bpt_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/cirtree_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bbi_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bigwig_file.c' Cython extension (up-to-date) skipping 'lib/bx/bbi/bigbed_file.c' Cython extension (up-to-date) skipping 'lib/bx/align/_epo.c' Cython extension (up-to-date) skipping 'lib/bx/arrays/bed.c' Cython extension (up-to-date) skipping 'lib/bx/arrays/wiggle.c' Cython extension (up-to-date) skipping 'lib/bx/align/sitemask/_cpg.c' Cython extension (up-to-date) skipping 'lib/bx/intseq/ngramcount.c' Cython extension (up-to-date) skipping 'lib/bx/misc/_seekbzip2.c' Cython extension (up-to-date) running build_scripts running install_lib creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9 creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages copying build/lib.dragonfly-6.5-x86_64-cpython-39/psyco_full.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/binned_array.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/binned_array_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bitset_builders.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bitset_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bitset_utils.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/filter.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/gene_reader.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/interval_index_file.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/interval_index_file_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seqmapping.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seqmapping_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/wiggle.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/wiggle_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/axt.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/core.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/epo.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/epo_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/lav.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/lav_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/maf.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/maf_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/score.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/score_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/sitemask/_cpg.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/sitemask/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/sitemask/core.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/sitemask/cpg.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/sitemask/quality.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/sitemask/sitemask_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/tools copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/tools/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/tools copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/tools/chop.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/tools copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/tools/fuse.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/tools copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/tools/thread.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/tools copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/tools/tile.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/tools copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/_core.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/align/_epo.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/arrays copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/arrays/array_tree.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/arrays copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/arrays/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/arrays copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/arrays/array_tree_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/arrays copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/arrays/wiggle.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/arrays copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/arrays/bed.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/arrays creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/bbi copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bbi/bigwig_file.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/bbi copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bbi/bigbed_file.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/bbi copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bbi/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/bbi copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bbi/bigwig_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/bbi copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bbi/bpt_file.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/bbi copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bbi/cirtree_file.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/bbi copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bbi/bbi_file.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/bbi creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/cookbook copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/cookbook/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/cookbook copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/cookbook/argparse.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/cookbook copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/cookbook/attribute.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/cookbook copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/cookbook/doc_optparse.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/cookbook copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/cookbook/progress_bar.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/cookbook creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/cluster_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/intersection_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/io.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/random_intervals.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations/base_coverage.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations/complement.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations/concat.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations/coverage.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations/find_clusters.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations/intersect.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations/join.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations/merge.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations/quicksect.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/operations/subtract.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/cluster.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intervals/intersection.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intseq copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intseq/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intseq copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/intseq/ngramcount.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intseq creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc/bgzf_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc/binary_file.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc/cdb.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc/cdb_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc/filecache.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc/filecache_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc/readlengths.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc/seekbzip2.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc/seekbzip2_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc/seeklzop.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc/seeklzop_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc/_seekbzip2.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/misc/bgzf.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/motif copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif/_pwm.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/motif copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/motif copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif/pwm.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/motif copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif/pwm_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/motif creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/motif/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif/io/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/motif/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif/io/transfac.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/motif/io copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif/io/transfac_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/motif/io creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/motif/logo copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif/logo/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/motif/logo copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/motif/logo/template.ps -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/motif/logo creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/phylo copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/phylo/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/phylo copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/phylo/newick.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/phylo copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/phylo/newick_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/phylo copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/phylo/phast.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/phylo copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/phylo/phast_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/phylo creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm/bed_score_aligned_pwm.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm/bed_score_aligned_string.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm/maf_select_motifs.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm/position_weight_matrix.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm/pwm_score_maf.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm/pwm_score_motifs.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm/pwm_score_positions.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm/pwm_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/pwm/_position_weight_matrix.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq/_nib.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq/core.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq/fasta.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq/fasta_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq/nib.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq/nib_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq/qdna.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq/qdna_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq/seq.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq/seq_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq/twobit.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq/twobit_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/seq/_twobit.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/tabular copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/tabular/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/tabular copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/tabular/io.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/tabular copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/_seqmapping.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx/bitset.cpython-39.so -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx creating /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx_extras copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx_extras/__init__.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx_extras copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx_extras/fpconst.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx_extras copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx_extras/fpconst_tests.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx_extras copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx_extras/lrucache.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx_extras copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx_extras/pstat.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx_extras copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx_extras/pyparsing.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx_extras copying build/lib.dragonfly-6.5-x86_64-cpython-39/bx_extras/stats.py -> /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx_extras byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/psyco_full.py to psyco_full.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/binned_array.py to binned_array.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/binned_array_tests.py to binned_array_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/bitset_builders.py to bitset_builders.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/bitset_tests.py to bitset_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/bitset_utils.py to bitset_utils.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/filter.py to filter.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/gene_reader.py to gene_reader.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/interval_index_file.py to interval_index_file.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/interval_index_file_tests.py to interval_index_file_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seqmapping.py to seqmapping.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seqmapping_tests.py to seqmapping_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/wiggle.py to wiggle.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/wiggle_tests.py to wiggle_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/axt.py to axt.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/core.py to core.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/epo.py to epo.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/epo_tests.py to epo_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/lav.py to lav.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/lav_tests.py to lav_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/maf.py to maf.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/maf_tests.py to maf_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/score.py to score.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/score_tests.py to score_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask/core.py to core.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask/cpg.py to cpg.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask/quality.py to quality.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/sitemask/sitemask_tests.py to sitemask_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/tools/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/tools/chop.py to chop.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/tools/fuse.py to fuse.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/tools/thread.py to thread.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/align/tools/tile.py to tile.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/arrays/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/arrays/array_tree_tests.py to array_tree_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/bbi/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/bbi/bigwig_tests.py to bigwig_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/cookbook/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/cookbook/argparse.py to argparse.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/cookbook/attribute.py to attribute.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/cookbook/doc_optparse.py to doc_optparse.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/cookbook/progress_bar.py to progress_bar.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/cluster_tests.py to cluster_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/intersection_tests.py to intersection_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/io.py to io.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/random_intervals.py to random_intervals.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/base_coverage.py to base_coverage.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/complement.py to complement.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/concat.py to concat.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/coverage.py to coverage.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/find_clusters.py to find_clusters.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/intersect.py to intersect.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/join.py to join.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/merge.py to merge.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/quicksect.py to quicksect.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intervals/operations/subtract.py to subtract.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/intseq/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc/bgzf_tests.py to bgzf_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc/binary_file.py to binary_file.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc/cdb.py to cdb.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc/cdb_tests.py to cdb_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc/filecache.py to filecache.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc/filecache_tests.py to filecache_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc/readlengths.py to readlengths.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc/seekbzip2.py to seekbzip2.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc/seekbzip2_tests.py to seekbzip2_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc/seeklzop.py to seeklzop.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/misc/seeklzop_tests.py to seeklzop_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/motif/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/motif/pwm.py to pwm.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/motif/pwm_tests.py to pwm_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/motif/io/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/motif/io/transfac.py to transfac.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/motif/io/transfac_tests.py to transfac_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/motif/logo/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/phylo/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/phylo/newick.py to newick.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/phylo/newick_tests.py to newick_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/phylo/phast.py to phast.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/phylo/phast_tests.py to phast_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm/bed_score_aligned_pwm.py to bed_score_aligned_pwm.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm/bed_score_aligned_string.py to bed_score_aligned_string.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm/maf_select_motifs.py to maf_select_motifs.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm/position_weight_matrix.py to position_weight_matrix.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm/pwm_score_maf.py to pwm_score_maf.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm/pwm_score_motifs.py to pwm_score_motifs.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm/pwm_score_positions.py to pwm_score_positions.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/pwm/pwm_tests.py to pwm_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq/core.py to core.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq/fasta.py to fasta.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq/fasta_tests.py to fasta_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq/nib.py to nib.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq/nib_tests.py to nib_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq/qdna.py to qdna.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq/qdna_tests.py to qdna_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq/seq.py to seq.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq/seq_tests.py to seq_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq/twobit.py to twobit.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/seq/twobit_tests.py to twobit_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/tabular/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx/tabular/io.py to io.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx_extras/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx_extras/fpconst.py to fpconst.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx_extras/fpconst_tests.py to fpconst_tests.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx_extras/lrucache.py to lrucache.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx_extras/pstat.py to pstat.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx_extras/pyparsing.py to pyparsing.cpython-39.pyc byte-compiling /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx_extras/stats.py to stats.cpython-39.pyc writing byte-compilation script '/tmp/tmp8z1x_iuk.py' /usr/local/bin/python3.9 /tmp/tmp8z1x_iuk.py removing /tmp/tmp8z1x_iuk.py running install_egg_info running egg_info writing lib/bx_python.egg-info/PKG-INFO writing dependency_links to lib/bx_python.egg-info/dependency_links.txt writing requirements to lib/bx_python.egg-info/requires.txt writing top-level names to lib/bx_python.egg-info/top_level.txt reading manifest file 'lib/bx_python.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'lib/bx_python.egg-info/SOURCES.txt' Copying lib/bx_python.egg-info to /construction/biology/py-bx-python/stage/usr/local/lib/python3.9/site-packages/bx_python-0.8.13-py3.9.egg-info running install_scripts copying build/scripts-3.9/aggregate_scores_in_intervals.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/align_print_template.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/axt_extract_ranges.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/axt_to_fasta.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/axt_to_lav.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/axt_to_maf.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/bed_bigwig_profile.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/bed_build_windows.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/bed_complement.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/bed_count_by_interval.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/bed_count_overlapping.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/bed_coverage.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/bed_coverage_by_interval.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/bed_diff_basewise_summary.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/bed_extend_to.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/bed_intersect.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/bed_intersect_basewise.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/bed_merge_overlapping.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/bed_rand_intersect.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/bed_subtract_basewise.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/bnMapper.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/div_snp_table_chr.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/find_in_sorted_file.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/gene_fourfold_sites.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/get_scores_in_intervals.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/int_seqs_to_char_strings.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/interval_count_intersections.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/interval_join.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/lav_to_axt.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/lav_to_maf.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/line_select.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/lzop_build_offset_table.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/mMK_bitset.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_build_index.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_chop.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_chunk.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_col_counts.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_col_counts_all.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_count.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_covered_ranges.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_covered_regions.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_div_sites.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_drop_overlapping.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_extract_chrom_ranges.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_extract_ranges.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_extract_ranges_indexed.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_filter.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_filter_max_wc.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_gap_frequency.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_gc_content.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_interval_alignibility.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_limit_to_species.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_mapping_word_frequency.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_mask_cpg.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_mean_length_ungapped_piece.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_percent_columns_matching.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_percent_identity.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_print_chroms.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_print_scores.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_randomize.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_region_coverage_by_src.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_select.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_shuffle_columns.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_species_in_all_files.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_split_by_src.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_thread_for_species.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_tile.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_tile_2.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_tile_2bit.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_to_axt.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_to_concat_fasta.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_to_fasta.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_to_int_seqs.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_translate_chars.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_truncate.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/maf_word_frequency.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/mask_quality.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/nib_chrom_intervals_to_fasta.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/nib_intervals_to_fasta.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/nib_length.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/one_field_per_line.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/out_to_chain.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/prefix_lines.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/pretty_table.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/qv_to_bqv.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/random_lines.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/table_add_column.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/table_filter.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/tfloc_summary.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/ucsc_gene_table_to_intervals.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/wiggle_to_array_tree.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/wiggle_to_binned_array.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/wiggle_to_chr_binned_array.py -> /construction/biology/py-bx-python/stage/usr/local/bin copying build/scripts-3.9/wiggle_to_simple.py -> /construction/biology/py-bx-python/stage/usr/local/bin changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/aggregate_scores_in_intervals.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/align_print_template.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/axt_extract_ranges.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/axt_to_fasta.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/axt_to_lav.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/axt_to_maf.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_bigwig_profile.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_build_windows.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_complement.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_count_by_interval.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_count_overlapping.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_coverage.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_coverage_by_interval.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_diff_basewise_summary.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_extend_to.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_intersect.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_intersect_basewise.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_merge_overlapping.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_rand_intersect.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bed_subtract_basewise.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/bnMapper.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/div_snp_table_chr.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/find_in_sorted_file.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/gene_fourfold_sites.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/get_scores_in_intervals.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/int_seqs_to_char_strings.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/interval_count_intersections.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/interval_join.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/lav_to_axt.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/lav_to_maf.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/line_select.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/lzop_build_offset_table.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/mMK_bitset.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_build_index.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_chop.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_chunk.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_col_counts.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_col_counts_all.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_count.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_covered_ranges.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_covered_regions.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_div_sites.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_drop_overlapping.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_extract_chrom_ranges.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_extract_ranges.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_extract_ranges_indexed.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_filter.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_filter_max_wc.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_gap_frequency.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_gc_content.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_interval_alignibility.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_limit_to_species.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_mapping_word_frequency.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_mask_cpg.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_mean_length_ungapped_piece.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_percent_columns_matching.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_percent_identity.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_print_chroms.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_print_scores.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_randomize.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_region_coverage_by_src.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_select.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_shuffle_columns.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_species_in_all_files.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_split_by_src.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_thread_for_species.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_tile.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_tile_2.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_tile_2bit.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_to_axt.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_to_concat_fasta.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_to_fasta.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_to_int_seqs.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_translate_chars.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_truncate.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/maf_word_frequency.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/mask_quality.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/nib_chrom_intervals_to_fasta.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/nib_intervals_to_fasta.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/nib_length.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/one_field_per_line.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/out_to_chain.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/prefix_lines.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/pretty_table.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/qv_to_bqv.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/random_lines.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/table_add_column.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/table_filter.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/tfloc_summary.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/ucsc_gene_table_to_intervals.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/wiggle_to_array_tree.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/wiggle_to_binned_array.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/wiggle_to_chr_binned_array.py to 755 changing mode of /construction/biology/py-bx-python/stage/usr/local/bin/wiggle_to_simple.py to 755 writing list of installed files to '/construction/biology/py-bx-python/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:06 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for py39-bx-python-0.8.13_1 file sizes/checksums [471]: 0% file sizes/checksums [471]: 21% file sizes/checksums [471]: 42% file sizes/checksums [471]: 63% file sizes/checksums [471]: 84% file sizes/checksums [471]: 100% Service unavailablepacking files [471]: 0% packing files [471]: 21% packing files [471]: 42% packing files [471]: 63% packing files [471]: 84% packing files [471]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:01 TOTAL TIME 00:02:00